Lobstermen fish off the Cutler coast in September 2006. Grand Manan Island is in the background. Cooke Aquaculture has been fined $490,000 after a pesticide it used killed hundreds of lobsters near Grand Manan Island in 2009, alarming Maine lobstermen.

A Canadian firm that is a subsidiary of the largest aquaculture operator in Maine pleaded guilty Friday in a Canadian courtroom to using illegal pesticides that killed hundreds of lobsters a little more than a mile from Maine’s border.

Cooke Aquaculture, based in Blacks Harbour, New Brunswick, agreed Friday to pay $100,000 in fines and an additional $400,000 in penalties that will fund environmental research and study at University of New Brunswick and restoration and enhancement of fish habitat in the Bay of Fundy region, according to Canadian court documents. The total amount, $500,000 in Canadian currency, is about $490,000 in U.S. currency.

Environment Canada has been investigating Cooke Aquaculture subsidiary Kelly Cove Salmon Ltd. in connection with the 2009 lobster deaths off Deer Island and Grand Manan Island, both of which are easily visible from Maine. According to Canadian court documents, four fishermen found dead lobsters in their traps off Grand Manan in November 2009, and the following month, two more fishermen found several hundred pounds of dead lobsters they had stored in Clam Cove by Deer Island. Clam Cove is roughly a mile and a half away from Pleasant Point in Maine.

In both cases, the dead and dying lobsters eventually were found to have been exposed to cypermethrin, a pesticide that is banned in Canada but which can be used in Maine with advance approval from state officials. Officials believe the cypermethrin was applied in salmon pens to combat the spread of sea lice, parasitic crustaceans that weaken the farmed fish and expose them to infection and disease.

In Maine, Cooke rotates its operations among two dozen salmon aquaculture sites in Hancock and Washington counties that are licensed to several subsidiary companies. The firm also has used legal sea lice treatments in Maine and New Brunswick within the past several years, according to industry officials.

According to a Cooke official, the court case in New Brunswick has no bearing on the company’s operations in Maine.

John Drouin, a Cutler lobsterman who is chairman of the Zone A Lobster Council, said Saturday that the fact that Maine’s largest aquaculture operator pleaded guilty in Canada to using a banned pesticide that killed lobsters is “not good.” He said Maine lobstermen in the zone, which abuts the Canadian border, were alarmed when they first heard about the New Brunswick lobster deaths.

Drouin said, in his experience, Maine Department of Marine Resources has done a good job of monitoring aquaculture lease sites that dot Machias and Cobscook bays, all of which now are owned by Cooke. There have been no similar reports about lobster deaths in Maine, he said, but the New Brunswick incident and resulting conviction indicates that continued vigilance is needed.

“I’m really hoping the state has done its job,” Drouin said. “You’ve got to keep your fingers crossed and hope people are doing the proper things.”

At the time, Environment Canada officials accused the company and each of the three Cooke officials of releasing cypermethrin into Passamaquoddy Bay and in the ocean off Grand Manan. When the charges initially were filed, each party faced possible penalties of a fine of up to $1 million for the first charge and an additional $1 million fine or 3 years in prison — or both — for each subsequent charge, Environment Canada officials have said.

As part of an agreement with Cooke officials, Canadian prosecutors dropped those original charges on Friday and instead charged Kelly Cove Salmon, but none of Cooke’s individual officers, with two charges of using cypermethrin in waters frequented by fish. The firm pleaded guilty to each charge and agreed to pay a $50,000 fine for each one, plus the $400,000 in additional penalties.

In a prepared statement released friday, Environment Canada officials said the $500,000 total represents one of the largest financial judgments ever levied in Canada for violating the Fisheries Act. Cypermethrin is banned in Canada, the agency indicated, because of its proven toxicity to crustaceans such as lobster and shrimp.

“Cooke used the pesticide to address a major sea lice infestation in their open pen salmon farm, knowing that it was illegal to do so,” Environment Canada officials wrote in the release.

It is not the first time pesticide use has been linked to lobster deaths in southwestern New Brunswick. In 1996 approximately 50,000 lobsters died in a pound near St. George, N.B., after being exposed to cypermethrin, and many people suspected the area’s aquaculture industry was responsible, the CBC has reported.

In 2010, with the state’s approval, Cooke used cypermethrin once at five Maine aquaculture sites in Cobscook Bay and Western Passage. Even though there have been no suspicious lobster deaths reported in Maine, the possibility of Maine lobsters being affected by pesticides has been a concern in the state’s lobstering community for more than a decade.

In 1999, the Long Island Sound lobster population plummeted after anti-mosquito pesticides were sprayed in the New York City area to fight the spread of West Nile virus. Long Island Sound fishermen later sued the pesticide manufacturers and then settled out of court for more than $16 million. And just last month, voters in the offshore Maine town of Cranberry Isles, where lobstermen make up a sizeable portion of the population, cited the possible impact on lobsters when they defeated a proposal to consider using pesticides to combat the islands’ mosquito population.

David Cousens, president of Maine Lobstermen’s Association, said Friday that the fact that Cooke pleaded guilty to using a banned pesticide that killed lobsters is a cause for concern. He said MLA and most lobstermen take a dim view of using any kind of pesticides, especially in the marine environment, because poisons that kill insects also tend to kill lobsters.

“It bears watching, obviously,” Cousens said of how pesticides are used at aquaculture sites. “We’re not for anything that will harm lobsters anywhere, here or in Canada.”

In 2010, the most recent year for which such information is available, farmed salmon sales in Maine were second only to the state’s lobster trap fishery in terms of commercial value. Salmon aquaculture brought in more than $76 million in direct revenue to Maine’s economy that year, while Maine lobstermen earned more than $318 million, according to DMR statistics.

Last year, Maine lobstermen harvested 126 million pounds and earned gross revenues of nearly $339 million, both of which are record amounts.

After 2010, Maine officials stopped publicly releasing information about the financial value of Maine’s annual farmed salmon harvest because Cooke is the only salmon aquaculture operator in Maine and Cooke officials successfully argued that such information was proprietary to their company.

According to an agreed statement of facts accepted Friday in New Brunswick Provincial Court by Judge Julian Dickson, Canadian investigators found that cypermethrin had been used between May and November 2010 at more than a dozen aquaculture sites in eastern New Brunswick, three of which are just across the border from Maine. In all, Kelly Cove Salmon has more than 100 marine aquaculture lease sites in eastern New Brunswick, court documents indicate.

According to the statement, supplier records indicate that Kelly Cove Salmon acquired 72 gallons of a cypermethrin-based pesticide in 2009.

In a prepared statement posted Friday on the Cooke Aquaculture website, CEO Glenn Cooke said the firm decided not to continue to fight the charges, “even though we question the allegations,” in order to spare the company, its employees and customers from a lengthy and public court battle.

“We want to resolve this matter today and move on,” Cooke said in the statement.

He added the company has invested millions of dollars on other sea lice treatments such as hydrogen peroxide baths in well-boats, on trials of using native cunner fish to clean salmon of the parasites, and on experimenting with lice traps and boosting resistance in salmon through selective breeding. The firm is committed to improving its internal protocols, to auditing procedures and to seeking out the best science available for its business, he said.

“Fish health is at the core of our business as farmers, as is the sustainability and health of our farms and the marine environment on which we depend,” Cooke said.

Nell Halse, spokeswoman for Cooke Aquaculture, on Friday declined to comment on the court-approved agreement or any of its specifics. She did say that no one at Cooke or Kelly Cove Salmon has lost his or her job over the company’s use of cypermethrin.

Halse said that sea lice appear naturally in certain areas and that, in 2009 and 2010, the options available in the U.S. and Canada for treating sea lice were insufficient.

“We didn’t have anything that was effective, and that was the issue,” she said.

Halse said that in other aquaculture-intensive countries such as Norway, Scotland and Chile, fish farmers are permitted to use a variety of chemical treatments so that, as sea lice build up resistance to one, they can switch to another. In Canada and the U.S., she said, prohibitions on some pesticides that can be used in other land-based applications makes it difficult for aquaculture companies.

“We’re woefully behind in North America,” Halse said.

Halse added that with the money the company is paying toward marine environmental research, perhaps new and effective treatments can be found and approved for use.

“That’s one of the solutions in all of this,” she said. “We need the governments and companies to work together.”

Matthew Abbott of the St. Andrew’s, N.B., environmental watchdog group Fundy Baykeeper said Friday that his group applauds Environment Canada for pursuing the case and getting a conviction. But he said that Canadian officials need to do more to assess the impact that pesticide use has on the environment.

“It highlights how deep rooted the problem is,” he said of violation and resulting penalties. “Any ocean waters need to treated with great care. We’re not convinced the existing rules are adequate.”

Greg Thompson, president of the Fundy North Fishermen’s Association in New Brunswick, said Friday that the group is pleased the matter was resolved but that lobstermen still find the case upsetting.

“There are other ways of dealing with [sea lice] than by using illegal pesticides,” Thompson said. “I think it’s a very serious offense.”